Remote Buddy does not make any changes to the OS install itself, so 
I'm afraid that once you have uninstalled all components as outlined 
in the FAQ015E0188 and rebooted, there's nothing that would be 
different from before installing Remote Buddy.

What you may find useful, though, is the list of general error sources 
with the Apple Remote in FAQ015E0222 that do apply regardless of 
whether or not you have Remote Buddy installed or ever had it installed.

Beyond that, please turn to the Plex team for help and assistance as 
it can only be a Plex-internal issue then and I naturally don't 
overlook that project as well as they do.

Best regards, 
Felix Schwarz